util.cc File Reference

Nonmember functions for evaluating some or all energy methods on residues or residue pairs. More...

#include <core/scoring/util.hh>
#include <core/scoring/EnergyMap.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/methods/ContextIndependentTwoBodyEnergy.hh>
#include <core/scoring/methods/ContextDependentTwoBodyEnergy.hh>
#include <core/types.hh>
#include <core/conformation/Residue.hh>
#include <utility/excn/Exceptions.hh>
#include <utility/options/OptionCollection.hh>
#include <utility/string_util.hh>
#include <utility/vector1.hh>
#include <basic/Tracer.hh>
#include <basic/options/keys/OptionKeys.hh>
#include <basic/options/keys/corrections.OptionKeys.gen.hh>
#include <basic/options/keys/mistakes.OptionKeys.gen.hh>
#include <numeric/xyzVector.hh>

Namespaces
	core
	A class for reading in the atom type properties.
	core::scoring

Functions
static basic::Tracer	TR ("core.scoring.utils")
void	core::scoring::eval_scsc_sr2b_energies (conformation::Residue const &r1, conformation::Residue const &r2, Vector const &r1sc_centroid, Vector const &r2sc_centroid, Real const &r1sc_radius, Real const &r2sc_radius, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap)
	With two bounding spheres for a pair of sidechains, evaluate all the sidechain/sidechain energies. This will avoid a call to EnergyMethod E's sidechain_sidechain_energiy method if a) E's atomic_interaction_cutoff + r1sc_radius + r2sc_radius < dist( r1sc_centroid, r2sc_centroid ) and b) E returns "true" in a call to its divides_backbone_and_- sidechain_energetics() method. Both context-dependent and context-independent 2-body energies are evaluated in this function. More...
void	core::scoring::eval_bbsc_sr2b_energies (conformation::Residue const &r1, conformation::Residue const &r2, Vector const &r1bb_centroid, Vector const &r2sc_centroid, Real const &r1bb_radius, Real const &r2sc_radius, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap)
	With two bounding spheres for a backbone and a sidechain, evaluate all the backbone/sidechain energies. This will avoid a call to EnergyMethod E's backbone_sidechain_energiy method if either a) E's atomic_interaction_cutoff + r1bb_radius + r2sc_radius < dist( r1bb_centroid, r2sc_centroid ) or b) E returns "false" in a call to its divides_backbone_and_- sidechain_energetics() method. The reason the call is avoided if "false" is returned is that, the entirety of a residue-pair-energy evaluation should be returned in the sidechain_sidechain_energy evaluation, if E does not implement its own versions of the bb/bb, bb/sc and sc/sc energy evaluation methods. Both context-dependent and context-independent 2-body energies are evaluated in this function. More...
void	core::scoring::eval_bbbb_sr2b_energies (conformation::Residue const &r1, conformation::Residue const &r2, Vector const &r1bb_centroid, Vector const &r2bb_centroid, Real const &r1bb_radius, Real const &r2bb_radius, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap)
	With two bounding spheres for a pair of backbones, evaluate all the backbone/sidechain energies. This will avoid a call to EnergyMethod E's backbone_backbone_energiy method if either a) E's atomic_interaction_cutoff + r1bb_radius + r2bb_radius < dist( r1bb_centroid, r2sc_centroid ) or b) E returns "false" in a call to its divides_backbone_and_- sidechain_energetics() method. The reason the call is avoided if "false" is returned is that, the entirety of a residue-pair-energy evaluation should be returned in the sidechain_sidechain_energy evaluation, if E does not implement its own versions of the bb/bb, bb/sc and sc/sc energy evaluation methods. Both context-dependent and context-independent 2-body energies are evaluated in this function. More...
Vector	core::scoring::compute_bb_centroid (conformation::Residue const &r1)
	Compute the average coordinate of the backbone heavy atoms (aka center of mass). More...
Real	core::scoring::compute_bb_radius (conformation::Residue const &r1, Vector const &r1bb_centroid)
	Given a representative point for the center of the backbone, compute the largest distance of all backbone heavy atoms to that point. More...
Vector	core::scoring::compute_sc_centroid (conformation::Residue const &r1)
	Compute the average coordiante of the sidechain atoms, (aka center of mass) or, if there are no side chain heavy atoms, compute the center of mass of the backbone. More...
Real	core::scoring::compute_sc_radius (conformation::Residue const &r1, Vector const &r1sc_centroid)
	Given a representative point for the center of the sidechain, compute the largest distance of all sidechain heavy atoms to that point. More...
bool	core::scoring::check_score_function_sanity (utility::options::OptionCollection const &options, std::string const &scorefxn_key, bool throw_exception=false)
	Check if a score function is requested with incompatible option flags Will return true if scorefunction is "sane" and false if not. If throw_exception is true, will raise an exception instead of returning false. More...

Detailed Description

Nonmember functions for evaluating some or all energy methods on residues or residue pairs.

Author

Andrew Leaver-Fay (aleav.nosp@m.erfa.nosp@m.y@gma.nosp@m.il.c.nosp@m.om)

Function Documentation

static basic::Tracer TR ( "core.scoring.utils"  )

static